Reference managers

(Modified 2014 Sep 17)

Office suites

and bibliography databases

Reference managers

Basically, my goal is to avoid copying and pasting from PubMed and formatting by hand.

• • Bibus

    • Pros:

      • Can interface with OpenOffice

      • Tags/categories can be hierarchical.

      • Supports drag and drop

    • Cons:

      • Searches which should work (e.g., by PMID) often don't.

      • Needs to be restarted sometimes -- searches stop working altogether

      • Search button (Medline) sometimes needs to be clicked multiple times.

    • Nitpicks:

      • When formatting in OpenOffice, can't edit directly, so one needs to copy and paste.

      • For export, list apparently terminates at the first "unusual" character (non-UTF?), so be sure to use the utf_8 option. (Thanks to Ubuntu Forums for the tip!)

      • Sometimes redundant punctuation is added upon formatting, e.g., ".." or "?."

      • During search, a progress bar would be useful.

    • Other notes:

      • If a reference needs to be imported manually, MEDLINE XML seems to work best, preserving non-ASCII characters.

  • Referencer

    • Pros:

      • Searches generally work

      • Stable

    • Cons:

      • Can't interface with OpenOffice

      • Abstracts not stored

      • Tags can't be hierarchical.

    • Nitpicks:

      • Keyboard shortcut to store selected reference would be useful.

      • Would be useful if search function remembered previous pulldown value (i.e., PMID or DOI)

      • Drag and drop would be useful.

Bibus 1.5.2 incompatibility with LibreOffice 4

LibreOffice 4 uses Python 3.3 (somewhere), while Bibus uses Python 2.X, such that Bibus doesn't work after upgrade. An explanation, but not a solution, for the problem was given at Bibus's SourceForge page. I got the general strategy for getting around this problem from LinuxG.net, although the listed tarball doesn't exist anymore. So for lack of a better idea, I downloaded the binaries individually from Ubuntu Packages Search, and had to resolve dependencies the hard way, like I had to do in the Dark Ages with RPMs. (I searched the 'Quantal' release specifically for LibreOffice 3.6 binaries.) There was a lot of trial and error involved, but essentially, you'll need to uninstall the existing version of LibreOffice, plus any other package that might conflict. If you miss one, the installation will be unsuccessful, and when you try to uninstall the package that caused the conflict apt-get/Synaptic will tell you to repair things, which will re-install packages that you'll need to turn around and re-uninstall. It was a big pain.

In any case, here's a list of all the packages I needed to download and install (Keep in mind I'm using a 64-bit system.):

• • libboost-date-time1.49.0_1.49.0-3.1ubuntu1.2_amd64.deb

  • libcmis-0.2-2_0.2.3-1_amd64.deb

  • libexttextcat-1.0-0_3.3.1-2_amd64.deb

  • libexttextcat-data_3.3.1-2_all.deb

  • libhsqldb-java_1.8.0.10-13ubuntu1_all.deb

  • libhyphen0_2.8.3-2_amd64.deb

  • libmythes-1.2-0_1.2.2-1build1_amd64.deb

  • libpoppler28_0.20.4-0ubuntu1.2_amd64.deb

  • libreoffice_3.6.2~rc2-0ubuntu3_amd64.deb

  • libreoffice-base_3.6.2~rc2-0ubuntu3_amd64.deb

  • libreoffice-base-core_3.6.2~rc2-0ubuntu3_amd64.deb

  • libreoffice-calc_3.6.2~rc2-0ubuntu3_amd64.deb

  • libreoffice-common_3.6.2~rc2-0ubuntu3_all.deb

  • libreoffice-core_3.6.2~rc2-0ubuntu3_amd64.deb

  • libreoffice-draw_3.6.2~rc2-0ubuntu3_amd64.deb

  • libreoffice-gnome_3.6.2~rc2-0ubuntu3_amd64.deb

  • libreoffice-gtk_3.6.2~rc2-0ubuntu3_amd64.deb

  • libreoffice-impress_3.6.2~rc2-0ubuntu3_amd64.deb

  • libreoffice-java-common_3.6.2~rc2-0ubuntu3_all.deb

  • libreoffice-math_3.6.2~rc2-0ubuntu3_amd64.deb

  • libreoffice-pdfimport_1.0.6+LibO3.6.2~rc2-0ubuntu3_amd64.deb

  • libreoffice-presenter-console_1.1.1+LibO3.6.2~rc2-0ubuntu3_amd64.deb

  • libreoffice-style-human_3.6.2~rc2-0ubuntu3_all.deb

  • libreoffice-writer_3.6.2~rc2-0ubuntu3_amd64.deb

  • libxerces2-java_2.11.0-6_all.deb

  • python-uno_3.6.2~rc2-0ubuntu3_amd64.deb

  • uno-libs3_3.6.2~rc2-0ubuntu3_amd64.deb

  • ure_3.6.2~rc2-0ubuntu3_amd64.deb

Did I mention it was a pain?... At least I didn't need to install the files one-by-one. The command was simply (assuming those are the only *.deb files in your directory):

sudo dpkg -i *.deb

Pay close attention to the failed installations or configurations.

<rant on>

I see questions online about this topic going back eleven months, during which no one had solved the problem. I'm sympathetic towards the Bibus people, since it probably isn't a trivial change to keep up with, but I'm less sympathetic to the Ubuntu people, who made LibreOffice 4 the default, while not addressing the incompatibility with the version of Bibus that they chose to include. I like Ubuntu, but my brand loyalty doesn't extend to accepting loss of functionality. I took a short trip to Distrowatch to see if there's an alternative I might try.

<rant off>

Bibus connectivity with LibreOffice 3

After the difficulties above, I downgraded, not just LibreOffice, but Xubuntu, to Linux Lite, which is based on the previous LTS version of Ubuntu.

Linux Lite uses Bibus 1.5.2 and LibreOffice 3.5, but out of the box, they weren't connecting. The error message I got was:

Cannot connect to Openoffice. See Documentation. Cannot connect to Openoffice. See Documentation. Connector : couldn't connect to pipe OOo_pipe(10))

I found the solution on Bibus's Sourcefourge page. The steps were as follows:

• • Open LibreOffice

  • Under Tools > Options > Security > Macro Security, set it to Low (temporarily)

  • Open in LibreOffice /usr/share/bibus/Setup//UnoConnectionListener.odg

  • Click Get current connection state. It will probably say it isn't connected.

  • Further down the document, click the button Accept UNO connection

  • Check the connection state, as above.

  • Once there's a connection, you can restore the Macro Security level.

  • In Bibus, open the Tools > First Connection Wizard

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